A multi-institutional Proteomics Core will provide state-of-the-art analysis of protein expression associated with the biology of pathogenic microbes. This core will function to characterize the proteomes of pathogens and host cells to identify mechanisms of microbial pathogenesis. The Proteomics Core is designed to provide Regional Center of Excellence (RCE) investigators a battery of methodologies associated with protein expression analysis. These include, high-throughput two-dimensional gel electrophoresis (2D/SDS-PAGE) with robotic picking and processing of protein gel spots; high-performance image analysis; peptide mass fingerprinting with high mass accuracy matrix-assisted laser desorption/ionization time-of-flight mass spectrometers (MS) as well as tandem MS with nanoelectrospray and liquid chromatography capabilities; surface-enhanced laser desorption/ionization MS with an interface option to the Micromass QTOF2 MS; protein chip and bead-based diagnostic tools to identify and quantify the differential expression of key proteins in response to pathogens; high-throughput cell selection and flow cytometry technologies (e.g., LEAP(TM), Laser Enabled Analysis and Processing, Oncosis, Inc.); subcellular fractionation; protein-protein interaction using confocal microscopy and immunoprecipitation methods; isotope-coded affinity tag methods for quantitation of protein expression; and cell signaling analysis in combination with tandem MS methods. Our proteomics activities will be closely associated with the Computational Biology Core and will apply bioinformatics and systems biology analyses to correlate changes in protein expression with genomic data of changes in gene expression as a result of pathogenic infections. This combined investigative approach will provide a rational basis for the development of effective pharmacological and immunological intervention strategies. The RCE Proteomics Core builds on existing regional strengths in proteomics especially focused at the University of Texas Southwestern Medical Center at Dallas (UTSW), the University of Texas Medical Branch at Galveston (UTMB), University of Houston, University of Texas at Austin, Baylor College of Medicine in Houston, Rice University, and the Los Alamos National Laboratories. UTSW and UTMB have NIH/NHLBI funded Proteomics Centers. A highly interactive, collaborative, and synergistic network of scientists has been assembled to oversee quality control, to implement proper validation procedures, and to effectively disseminate results to RCE researchers, NIAID, and the scientific community at large.